That said, a person would be foolish to write the entire book using this. Write your text and create your graphics in your editors of choice, import them into this tool to create a nice layout for the iBookstore, then import them into another tool to create a nice layout for Kindle or whatever. You might have to do that anyway -- I've yet to see a tool that will generate a nicely-formatted ebook in both MOBI (Kindle) and ePub formats. Conversion tools like Calibre work if all you care about is reading the text, but the output often looks like ass if the original eBook used anything other than the most basic formatting (that said, a lot of commercially-produced eBooks look like ass anyway, so maybe that's not such a big deal).
For an anology, consider MS Word. When I create a document using MS Word and save it in one of Words native formats, this file includes all sorts of information generated by MS code and includes MS specific formatting information. That does not, in any traditional meaning of the word, mean that my essay is a derivative work of MS Word.
These files don't just contain "formatting information". They contain actual executable code created by Apple. Apple's claim lies on the distribution of their code, not your content per se. They can put any restrictions on the distribution of their code that they want, whether we like it or not (and I don't particularly like it myself). They're not claiming ownership of your essay. They're claiming ownership over the code they wrote, which their system uses to display it. Not the same thing.
What you, and others, are claiming is that this type of license has no legal effect. That's clearly wrong.
Let's not confuse the two issues of whether it's a good idea for Apple to do this (it isn't) and whether they're legally allowed to do it (they clearly are).
But a derivative work of the base template (normal.dot?), yes. If the template was released as NC-SA, then the resulting document is NC-SA.
Whether I personally believe in my gut if it is right that these books be deemed derivatives is a separate issue.. ;)
This is not an uncommon thing to see. IIRC, the gcc compilers have an explicit exception clause that says that programs compiled with gcc (e.g., the output) are not affected by the GNU GPL. A compiler usually does more than just transforms code from a higher-level language to a lower-level language. It can reorganize the code (-O2, -O3, -O4); it can inject standard or custom implementations of common behaviours that the user didn't explicitly write.
From a very real and very strict standpoint, a compiler/code generator does create a derivative work (and there's at least one code generator I've used in the past few years that holds this to be true explicitly; gSOAP) that is a combination of your copyrighted code and the code by the compiler writer (and possibly others involved).
There is no ground for any of this.